Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning

Journal of Chemical Information and Modeling
Nobuaki Yasuo, Masakazu Sekijima

Abstract

Virtual screening is a promising method for obtaining novel hit compounds in drug discovery. It aims to enrich potentially active compounds from a large chemical library for further biological experiments. However, the accuracy of current virtual screening methods is insufficient. In this study, we develop a new virtual screening method named Similarity of Interaction Energy VEctor Score (SIEVE-Score), in which protein-ligand interaction energies are extracted to represent docking poses for machine learning. SIEVE-Score offers substantial improvements compared to other state-of-the-art virtual screening methods, namely, other machine-learning-based scoring functions, interaction fingerprints, and docking software, for the enrichment factor 1% results on the Directory of Useful Decoys, Enhanced (DUD-E). The screening results are also human-interpretable in the form of important interactions for distinguishing between active and inactive compounds. The source code is available at https://github.com/sekijima-lab/SIEVE-Score .

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Citations

Aug 23, 2019·Bioinformatics·Aeri Lee, Dongsup Kim
Mar 27, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Igor SieradzkiSabina Podlewska
Dec 22, 2019·Scientific Reports·Shuntaro ChibaMasakazu Sekijima
Jun 5, 2020·Briefings in Bioinformatics·Guo-Li XiongDong-Sheng Cao
Jun 23, 2020·Briefings in Bioinformatics·Louison Fresnais, Pedro J Ballester
Dec 11, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ke-Jia WuDik-Lung Ma
Jul 29, 2020·Scientific Reports·Ryunosuke YoshinoMasakazu Sekijima
Oct 21, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Javier VázquezF Javier Luque
Dec 1, 2019·Drug Discovery Today. Technologies·Pedro J Ballester
Dec 24, 2020·Expert Opinion on Drug Discovery·Julio Caballero
Apr 30, 2021·Parasitology International·Nobuaki YasuoMasakazu Sekijima
May 31, 2021·Current Opinion in Chemical Biology·Ghita GhislatPedro J Ballester
Jun 16, 2021·Expert Opinion on Drug Discovery·AkshatKumar NigamAlán Aspuru-Guzik
Jul 3, 2021·International Journal of Molecular Sciences·Donghyuk SuhYoonji Lee
Jul 22, 2021·Computational and Structural Biotechnology Journal·Alexander D H Kingdon, Luke J Alderwick
Jul 28, 2021·Journal of Chemical Information and Modeling·Manuel A LlanosLuciana Gavernet
Aug 6, 2019·Journal of Chemical Information and Modeling·Florian LeidnerCelia A Schiffer
Apr 2, 2020·Journal of Chemical Information and Modeling·Hugo Guterres, Wonpil Im
Sep 22, 2021·Expert Opinion on Drug Discovery·Juan I Di Filippo, Claudio N Cavasotto
Nov 16, 2019·Current Medicinal Chemistry·Gabriela Bitencourt-FerreiraWalter Filgueira de Azevedo
Sep 25, 2021·Drug Discovery Today·Kevin CramponLuiz Angelo Steffenel
Oct 19, 2021·Experimental and Therapeutic Medicine·Ayumu AsaiHideshi Ishii

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